5A3I

Crystal Structure of a Complex formed between FLD194 Fab and Transmissible Mutant H5 Haemagglutinin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 

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Literature

Structures of Complexes Formed by H5 Influenza Hemagglutinin with a Potent Broadly Neutralizing Human Monoclonal Antibody.

Xiong, X.Corti, D.Liu, J.Pinna, D.Foglierini, M.Calder, L.J.Martin, S.R.Lin, Y.P.Walker, P.A.Collins, P.J.Monne, I.Suguitan, A.L.J.Santos, C.Temperton, N.J.Subbarao, K.Lanzavecchia, A.Gamblin, S.J.Skehel, J.J.

(2015) Proc Natl Acad Sci U S A 112: 9430

  • DOI: https://doi.org/10.1073/pnas.1510816112
  • Primary Citation of Related Structures:  
    5A3I

  • PubMed Abstract: 

    H5N1 avian influenza viruses remain a threat to public health mainly because they can cause severe infections in humans. These viruses are widespread in birds, and they vary in antigenicity forming three major clades and numerous antigenic variants. The most important features of the human monoclonal antibody FLD194 studied here are its broad specificity for all major clades of H5 influenza HAs, its high affinity, and its ability to block virus infection, in vitro and in vivo. As a consequence, this antibody may be suitable for anti-H5 therapy and as a component of stockpiles, together with other antiviral agents, for health authorities to use if an appropriate vaccine was not available. Our mutation and structural analyses indicate that the antibody recognizes a relatively conserved site near the membrane distal tip of HA, near to, but distinct from, the receptor-binding site. Our analyses also suggest that the mechanism of infectivity neutralization involves prevention of receptor recognition as a result of steric hindrance by the Fc part of the antibody. Structural analyses by EM indicate that three Fab fragments are bound to each HA trimer. The structure revealed by X-ray crystallography is of an HA monomer bound by one Fab. The monomer has some similarities to HA in the fusion pH conformation, and the monomer's formation, which results from the presence of isopropanol in the crystallization solvent, contributes to considerations of the process of change in conformation required for membrane fusion.


  • Organizational Affiliation

    Mill Hill Laboratory, The Francis Crick Institute, London NW7 1AA, United Kingdom;


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEMAGGLUTININ
A, E
328Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 0 
UniProt
Find proteins for Q6DQ33 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1))
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Go to UniProtKB:  Q6DQ33
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UniProt GroupQ6DQ33
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HEMAGGLUTININ166Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 0 
UniProt
Find proteins for A8UDR1 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1))
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Go to UniProtKB:  A8UDR1
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UniProt GroupA8UDR1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ANTI-HAEMAGGLUTININ HA1 FAB HEAVY CHAIN
C, G
230Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ANTI-HAEMAGGLUTININ HA1 FAB LIGHT CHAIN
D, H
219Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
HEMAGGLUTININ166Influenza A virus (A/Viet Nam/1203/2004(H5N1))Mutation(s): 0 
UniProt
Find proteins for A8UDR1 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1))
Explore A8UDR1 
Go to UniProtKB:  A8UDR1
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UniProt GroupA8UDR1
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Oligosaccharides

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Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I, J
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
K [auth E]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.75α = 78.67
b = 87.7β = 84.66
c = 100.9γ = 73.91
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2015-09-09
    Changes: Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary